## htsjdk.samtools.metrics.StringHeader # MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/joost/results/star/hg38-external-HS-029RNA-U2OS-1mM-EU-1hr-18672.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/joost/results/final_bam/hg38-external-HS-029RNA-U2OS-1mM-EU-1hr-18672.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/joost/results/qc/markdup/hg38-external-HS-029RNA-U2OS-1mM-EU-1hr-18672.samtools-coordinate.metrics.txt TMP_DIR=[/scratch/siebrenf/tmp/gN7y] MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Mon Mar 08 17:15:07 CET 2021 ## METRICS CLASS picard.sam.DuplicationMetrics LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED SECONDARY_OR_SUPPLEMENTARY_RDS UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE Unknown Library 41 964651 0 0 29 500146 89 0.518478 568907 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.000034 281021 0 281046 2.0 1.183526 81015 87 81008 3.0 1.217194 37892 1 37887 4.0 1.223371 21815 0 21809 5.0 1.224505 13663 0 13662 6.0 1.224713 8977 0 8971 7.0 1.224751 6056 0 6061 8.0 1.224758 4056 0 4057 9.0 1.224759 2822 0 2817 10.0 1.22476 1936 0 1937 11.0 1.22476 1294 0 1292 12.0 1.22476 836 0 838 13.0 1.22476 612 0 610 14.0 1.22476 484 0 485 15.0 1.22476 370 0 369 16.0 1.22476 266 0 266 17.0 1.22476 181 0 181 18.0 1.22476 157 0 157 19.0 1.22476 141 0 141 20.0 1.22476 77 0 77 21.0 1.22476 75 0 75 22.0 1.22476 73 0 73 23.0 1.22476 72 0 72 24.0 1.22476 47 0 47 25.0 1.22476 43 0 43 26.0 1.22476 40 0 40 27.0 1.22476 31 0 31 28.0 1.22476 27 0 27 29.0 1.22476 23 0 23 30.0 1.22476 26 0 26 31.0 1.22476 19 0 19 32.0 1.22476 24 0 24 33.0 1.22476 12 0 12 34.0 1.22476 11 0 11 35.0 1.22476 8 0 8 36.0 1.22476 13 0 14 37.0 1.22476 6 0 5 38.0 1.22476 9 0 9 39.0 1.22476 8 0 10 40.0 1.22476 8 0 6 41.0 1.22476 4 0 4 42.0 1.22476 5 0 5 43.0 1.22476 6 0 6 44.0 1.22476 5 0 5 45.0 1.22476 7 0 7 46.0 1.22476 4 0 4 47.0 1.22476 3 0 3 48.0 1.22476 4 0 4 49.0 1.22476 4 0 4 50.0 1.22476 2 0 2 51.0 1.22476 3 0 3 52.0 1.22476 1 0 1 53.0 1.22476 2 0 2 54.0 1.22476 2 0 2 55.0 1.22476 2 0 2 56.0 1.22476 1 0 1 57.0 1.22476 4 0 4 58.0 1.22476 0 0 0 59.0 1.22476 2 0 2 60.0 1.22476 3 0 3 61.0 1.22476 1 0 1 62.0 1.22476 3 0 3 63.0 1.22476 2 0 2 64.0 1.22476 1 0 1 65.0 1.22476 2 0 2 66.0 1.22476 0 0 0 67.0 1.22476 1 0 1 68.0 1.22476 0 0 0 69.0 1.22476 0 0 0 70.0 1.22476 2 0 2 71.0 1.22476 0 0 0 72.0 1.22476 1 0 1 73.0 1.22476 0 0 0 74.0 1.22476 0 0 0 75.0 1.22476 0 0 0 76.0 1.22476 0 0 0 77.0 1.22476 2 0 2 78.0 1.22476 0 0 0 79.0 1.22476 0 0 0 80.0 1.22476 0 0 0 81.0 1.22476 0 0 0 82.0 1.22476 2 0 2 83.0 1.22476 0 0 0 84.0 1.22476 0 0 0 85.0 1.22476 0 0 0 86.0 1.22476 0 0 0 87.0 1.22476 1 0 1 88.0 1.22476 0 0 0 89.0 1.22476 0 0 0 90.0 1.22476 0 0 0 91.0 1.22476 0 0 0 92.0 1.22476 0 0 0 93.0 1.22476 0 0 0 94.0 1.22476 0 0 0 95.0 1.22476 0 0 0 96.0 1.22476 1 0 1 97.0 1.22476 0 0 0 98.0 1.22476 0 0 0 99.0 1.22476 0 0 0 100.0 1.22476 0 0 0 159.0 0 1 0 1